Showing : Tcga • reset
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One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
12 days ago • updated 4 days ago glaciya2018 • 0
0
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1
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235
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TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks TCGA clinical TCGA-BRCA
written 8 weeks ago by • 0
1
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0
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177
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Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k MethylationArray TCGAbiolinks Tcga TCGAbiolinksGUI.data
10 weeks ago BioinfoMug • 0
0
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2
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542
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TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 6 months ago by ★ 1.0k • written 6 months ago by ▴ 190
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1
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513
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GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA GenomicDataCommons GDC
written 10 months ago by ▴ 510
1
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1
reply
497
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
1
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3
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1.0k
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Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2 recount GTEx TCGA recount3
updated 12 months ago by ★ 4.1k • written 12 months ago by ▴ 20
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1
reply
634
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TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 17 months ago by ★ 4.1k • written 17 months ago by • 0
2
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9
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2.3k
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Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
23 months ago • updated 22 months ago Peipei • 0
2
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2
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1.9k
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Create TPM gene tables/dataframe from ReCount3
recount3 TCGA GTEx DESeq2
23 months ago David ▴ 20
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1
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1.1k
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recount3 - download bigwig files for TCGA data
recount3 recount TCGA
updated 2.1 years ago by ★ 1.0k • written 2.1 years ago by ▴ 10
0
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2
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893
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Removing paired samples for DESeq2 analysis
RNASeq DifferentialExpression DESeq2 tcga
2.3 years ago IamFrofro • 0
3
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2
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1.1k
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How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons
TCGA GenomicDataCommons
updated 2.4 years ago by ★ 3.3k • written 2.4 years ago by ▴ 10
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0
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735
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Determine whether RNAseq data from TCGA is paired or single-end?
TCGA TCGAbiolinks
3.0 years ago rebeliscu • 0
0
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1
reply
820
views
Getting number of cases added by date to TCGA project with `GenomicDataCommons`
TCGA GenomicDataCommons
3.1 years ago Ezgi ▴ 60
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0
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959
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Job: PhD position in Developmental Neurobiology and Bioinformatics
rnaseq neurobiology tcga Job
3.5 years ago Laurent Gatto 1.6k
2
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5
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1.6k
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GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks TCGA
updated 2.0 years ago by • 0 • written 3.6 years ago by ▴ 40
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0
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724
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Identify significantly different DNA methylation probes in tumor and normal samples GBM ELMER R package
ELMER TCGA GEO
3.7 years ago andrade4beatriz • 0
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5
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2.8k
views
Retrieve TCGA expression data for a single gene
TCGA TCGAbiolinks
updated 3.7 years ago by ▴ 260 • written 3.7 years ago by ▴ 40
4
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7
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4.0k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
4
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7
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1.1k
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'NA' found under Gene Names in the list of top differentially expressed genes found using edgeR
edger differential expression TCGA Gene ID
updated 4.1 years ago by 65k • written 4.1 years ago by ▴ 60
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2
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1.4k
views
Recount2 Bigwigs for TCGA
R TCGA recount2 recount
updated 4.1 years ago by ★ 1.0k • written 4.2 years ago by • 0
0
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0
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716
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Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
4.4 years ago modarzi ▴ 10
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4
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1.2k
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
4.4 years ago modarzi ▴ 10
2
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3
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806
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DESeq2 doesn't return the most drastically DEG
deseq2 tcga
4.5 years ago ndjayne • 0
2
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2
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2.3k
views
DESeq2: design = ~1 For Normalisation Only.
deseq2 limma normalization tcga rnaseq
updated 4.5 years ago by 42k • written 4.5 years ago by • 0
1
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2
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1.2k
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TCGAbiolinks : Bisulfite-seq data : Legacy archive
tcga bisulfite tcgabiolinks
updated 4.8 years ago by ▴ 260 • written 4.8 years ago by • 0
1
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1
reply
1.3k
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TCGA isoform expression quantification file - how to reshape data
data.frame tcga reshape data
updated 5.0 years ago by ★ 13k • written 5.0 years ago by ▴ 160
1
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2
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1.3k
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TCGA MAF (Mutations) data
TCGA MAF GDC snp mutations
updated 5.0 years ago by 21k • written 5.0 years ago by ▴ 160
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1
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1.1k
views
How to download the TCGA SKCM subtype information?
TCGA melanoma TCGA SKCM
5.0 years ago syrttgump ▴ 20
5
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4
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1.9k
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Perform correlation analysis between miRNA and mRNA gene expression data on the same TCGA dataset based on the curatedTCGAData
curatedTCGAData MultiAssayExperiment multiomics TCGA
updated 5.1 years ago by ★ 1.1k • written 5.1 years ago by ▴ 830
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0
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980
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TCGAbiolinks specific mutation query
TCGAbiolinks TCGA Mutation GDCquery rnaseq
5.1 years ago Yonatan Amzaleg • 0
1
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3
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2.1k
views
Error via running GDCdownload() in TCGAbiolinks
TCGAbiolinks TCGA Download
updated 5.2 years ago by ▴ 260 • written 5.2 years ago by ▴ 10
4
votes
6
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3.6k
views
DESeq2 vst normalization: Do I have a heteroscedasticity problem and if so, what can I do about it?
deseq2 normalization rna-seq TCGA vst
updated 5.2 years ago by 42k • written 5.2 years ago by ▴ 70
1
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5
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1.6k
views
Issue with TCGAbiolinks package.
TCGA GDCprepare
5.2 years ago salvocomplicazioni1 • 0
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0
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816
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Reference for minimum number of probes commonly used for segmentation of microarray data
segmentation reference CNA TCGA
5.3 years ago jlarsen728 • 0
4
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2
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1.1k
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GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 5.3 years ago by 21k • written 5.3 years ago by ▴ 20
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1.0k
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Tumor subtype classification when genes of gene set are missing from samples - GSVA approach
GSVA geneset RNASeq TCGA subtypes
5.3 years ago Pietro ▴ 40
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0
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923
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GDC RNA seq files (replicates?)
gdc data TCGA gdcdownload
5.3 years ago coyoung ▴ 10
2
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4
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1.3k
views
edgeR. Known cancer genes are not differentially expressed?
edger tcga
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 30
3
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2
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2.2k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 2.1 years ago by • 0 • written 5.5 years ago by ▴ 10
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1
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1.1k
views
RNAseq gene expression analysis in Personalized genomics
TCGA deseq2 edger limma
updated 5.5 years ago by 42k • written 5.5 years ago by • 0
2
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3
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1.5k
views
Problem for finding "Locus Link ID" from Annotation file
wgcna package TCGA LocusLinkID genecode ensembl
updated 5.6 years ago by 65k • written 5.6 years ago by ▴ 10
8
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8
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6.8k
views
Voom transformation from counts and normalization to negative values
rnaseq voom limma tcga statistics
updated 5.6 years ago by ★ 7.9k • written 5.6 years ago by ▴ 60
8
votes
12
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6.2k
views
MultiAssayExperiment: Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
multiassayexperiment wide format TCGA
updated 5.6 years ago by 690 • written 5.6 years ago by ▴ 160
1
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2
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1.2k
views
how to output and get the normalization gene expression data (similar to the FPKM gene expression data) from reads count data by DESeq2 and edgeR?
deseq2 edger fpkm counts TCGA
updated 5.6 years ago by 50k • written 5.6 years ago by • 0
3
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4
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2.4k
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TCGA biolinks - Samples with multiple profiles
tcgabiolinks tcga genomicdatacommon
5.7 years ago franceschini.gianmarco • 0
0
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5
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2.1k
views
DNA methylation analysis without raw data IDAT files
r illimina 450k methylation minfi champ tcga
updated 5.7 years ago by ▴ 280 • written 5.7 years ago by ▴ 60
4
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2
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2.0k
views
Where to download expected counts instead of normalized RSEM for TCGA LUAD?
limma tcga
updated 5.7 years ago by ★ 13k • written 5.7 years ago by ▴ 50
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2
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2.6k
views
Error: vector memory exhausted (limit reached?)
tcgabiolinks tcga cnv mac os x gaia
updated 5.8 years ago by ▴ 20 • written 5.8 years ago by ▴ 30
50 results • Page 1 of 1
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Comment: Cannot connect to ExperimentHub server by Jiayu • 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea() by Chris • 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
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